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Hello Jasmijn, I am trying to run savage-ref mode using single and paired-end reads processed with PEAR, but get an error after running for an hour that seems to have something to do with the random_s…
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**run code just following: virsorter run -w out -i /home/dell/database/H1_assembly.contigs.fa --min-length 1000 -j 16 all**
[2024-06-20 00:55 INFO] VirSorter 2.2.3
[2024-06-20 00:55 INFO] /home/dell…
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Has there been any research on STAR's performance on non-mamallian transcriptomes such as protists?
What about mixed communities and metatranscriptomics?
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Hi,
I am trying to run contig extender on my contigs assembled using MegaHit, using default parameters and Bowtie2 v2.4.1.
I encounter the following error :
> ValueError: Buffer dtype mismat…
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## Expected Behavior
Taxonomy assignment of viral OTU sequences (nucleotide) using the 2bLCA method against a custom formatted amino acid database from IMG/VR
## Current Behavior
The LCA step die…
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We've had reasonably good results with [IVA], but it has a few problems:
1. Some samples are very slow, even taking multiple days. Random primers seem to be slow.
2. We find contigs with a lot of …
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is it possible to add a function to extract representative genomes/sequences from the fasta file?
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In viral taxonomy prediction section, we've provided the vConTACT2 output files rather than getting them to run it. But the file `vConTACT2_Results/tax_predict_table.tsv` (the output from `tax_predict…
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I successfully installed vironomy and downloaded the database.
Here is the database list:
`
full_sc_marker_db.csv
genbank_pfam_tgirfam_all_annotations_sc.txt
genbank_predicted_proteins.faa
g…